Analysis of the algorithm: From rankings to backup genes.

Ranking section

Table 1. Performance summary for every kernel and net before integration.

Net Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
biological_process ct 0.0837887067395264 0.116575591985428 0.000367559261549628 0.000701865209760493 0.12797619047619
biological_process el 0.0133495145631068 0.0266990291262136 0.0039606398404883 0.0111764431371956 0.00520198325611639
biological_process ka 0.13357619914997 0.170613236187007 0.000455704657393107 0.000798353263595665 0.173853989813243
biological_process rf 0.0837887067395264 0.117182756527019 0.000335713771746963 0.00070242573209431 0.12797619047619
cellular_component ct 0.0697815533980582 0.100121359223301 0.000460476754617662 0.00101540627191351 0.0968506603454115
cellular_component el 0.0333535476046089 0.0527592480291086 0.0326209040275033 0.053668329966965 0.00193923723335488
cellular_component ka 0.0703883495145631 0.0983009708737864 0.000446983502806492 0.00116530379613624 0.0987569060773481
cellular_component rf 0.0558252427184466 0.0849514563106796 0.000305278310040542 0.000659059390105018 0.0982286634460548
disease ct 0.347945205479452 0.415068493150685 0.00176322682510564 0.00219777796031116 0.223871849970697
disease el 0.178082191780822 0.218493150684931 0.00624148557834181 0.00807083512063935 0.0450617283950617
disease ka 0.289041095890411 0.358921232876712 0.000415552452488082 0.000663219827992711 0.3674228337672
disease rf 0.346575342465753 0.407534246575342 0.00169937056405857 0.00216133212861302 0.225273631840796
gene_PS ct 0.155490767735666 0.224514091350826 0.000802150365533896 0.00125218308234751 0.193849021435228
gene_PS ka 0.399805447470817 0.470817120622568 0.000922636812641577 0.00150829076228692 0.354312354312354
gene_PS rf 0.32295719844358 0.406639105058366 0.00104034661901471 0.00137551711346651 0.304783950617284
gene_TF ct 0.0285714285714286 0.114285714285714 0.0307697983275947 0.10315324916653 0.00516929439131559
gene_TF el 0 0.0214285714285714 0.0025031425916817 0.035098923320763 0.00505050505050505
gene_TF ka 0.0357142857142857 0.128571428571429 0.0440277094605673 1 0.00450704225352113
gene_TF rf 0.0928571428571429 0.214285714285714 0.0637161829808165 0.175386402142428 0.00600272851296044
gene_hgncGroup ct 0.0839469808541973 0.117083946980854 0.00104135722411007 0.00171589534095602 0.0832589949449896
gene_hgncGroup el 0.148857774502579 0.191599115696389 0.00126390802720085 0.00222768853396286 0.123949579831933
gene_hgncGroup ka 0.117170228445099 0.156963890935888 0.000489382737842744 0.00116398627837923 0.158995815899582
gene_hgncGroup rf 0.0957995578481945 0.131908621960206 0.000700819002653163 0.0011948454341623 0.113046569498756
genetic_interaction_effect_bicor ct 0.0323785803237858 0.0516967621419676 0.000593261901954268 0.00184306090070002 0.0431519699812383
genetic_interaction_effect_bicor el 0.00186799501867995 0.00933997509339975 0.000124888779305983 0.00261524071910209 0.00932159502848265
genetic_interaction_effect_bicor ka 0.0330012453300125 0.0510585305105853 0.000430397285679063 0.0010603754167426 0.0520361990950226
genetic_interaction_effect_bicor rf 0.0317559153175592 0.0529420921544209 0.000582032631883623 0.001877271314173 0.0431789737171464
molecular_function ct 0.0538885486834048 0.0796080832823025 0.000377606681208468 0.00110542225570987 0.0825190010857763
molecular_function el 0.00856793145654835 0.0195838433292534 0.00858204171008719 0.0223387856323128 0.00187083129982105
molecular_function ka 0.0642988364972443 0.091855480710349 0.000613093108684663 0.00131968430150283 0.0818494220556076
molecular_function rf 0.0545009185548071 0.0820728720146969 0.000345578838618719 0.00103322769949336 0.0861172976985895
pathway ct 0.139356814701378 0.209800918836141 0.00144372381648818 0.00282957053914969 0.133632790567097
pathway ka 0.193213190184049 0.273006134969325 0.000666247503387193 0.00153290744977302 0.250587314017228
pathway rf 0.167139570552147 0.234662576687117 0.000726132039850126 0.00146430932883188 0.208269525267994
phenotype ct 0.210277214334009 0.273833671399594 0.000623219934473963 0.000911702802727853 0.250754274220583
phenotype el 0.0310810810810811 0.0506756756756757 0.00127507630237388 0.00260088208636739 0.0282996984458362
phenotype ka 0.226504394861393 0.293441514536849 0.000405003006299849 0.000600665251634136 0.308575803981623
phenotype rf 0.211629479377958 0.270453008789723 0.000615756222683856 0.000890292952174557 0.251347708894879
protein_interaction ct 0.260216346153846 0.307091346153846 0.000956129931071146 0.00130997919568007 0.228639618138425
protein_interaction el 0.262605168269231 0.316721754807692 0.000682552865364557 0.000944326336676263 0.280022446689113
protein_interaction ka 0.259771497294047 0.307892363199038 0.00062831806236018 0.000964494082433261 0.272212790039615
protein_interaction rf 0.251802884615385 0.302899639423077 0.000804131180468038 0.00106947287965815 0.244357976653696

Table 2. Performance summary for every kernel after integration

Integration Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
integration_mean_by_presence ct 0.187350835322196 0.23090692124105 0.000672449362725385 0.000980750962272358 0.203351320647543
integration_mean_by_presence ka 0.324776119402985 0.373134328358209 0.000294939404058264 0.000509039764499862 0.39986399183951
integration_mean_by_presence rf 0.256716417910448 0.307462686567164 0.000544176023939847 0.000795079692626976 0.286556603773585
mean ct 0.245211813842482 0.292974343675418 0.000899129646195639 0.00133519136704227 0.225900681596884
mean ka 0.352835820895522 0.427477611940298 0.000413941041869598 0.000667358107217398 0.424922118380062
mean rf 0.285970149253731 0.341492537313433 0.000732950065989486 0.00110441983367469 0.283033620015637

Backup Pairs Coverage By Layer Non integrated

Backup Pairs Coverage By Layer Integrated

Distribution of ranks in dataset by non integrated kernels

Distribution of ranks in dataset by Integrated kernels

ROC-AUCs for Non-integrated kernel and layer

ROC-AUCS for integrated kernels

CDF plots of non integrated kernels

ROC plots of non integrated kernels

ROC plots of integrated kernels

CDF plots of integrated kernels